ga4gh/vrs: 1.3.0 Release: Genotype, Copy Changes, and Composed SEs

Release summary

The v1.3.0 release of VRS includes two new systemic variation concepts:

1. the Genotype model for representing all variants present at a given genomic locus
2. the CopyNumberChange model for representing copy number changes from a regional base ploidy

It also includes support for composed sequence expressions, for expressing sequences composed of multiple underlying expressions.

Additional minor changes include cleanup of the allele normalization guidance, haplotype member minimum, and updates to the processing tools (i.e. gks.metaschema) used to build and represent the schema artifacts. This has also enabled explicity class inheritance and explicit declaration of array ordinality for processing computed digests.

• remove ComposedSequenceExpression from 1.2, belongs in 1.3+ by @ahwagner in https://github.com/ga4gh/vrs/pull/380
• relative copy number by @ahwagner in https://github.com/ga4gh/vrs/pull/382
• Update validation models for Copy Number variation by @korikuzma in https://github.com/ga4gh/vrs/pull/383
• Fix Allele state type priority by @jsstevenson in https://github.com/ga4gh/vrs/pull/384
• 386: revise base64url description by @ahwagner in https://github.com/ga4gh/vrs/pull/387
• explain ref agree normalization rules by @reece in https://github.com/ga4gh/vrs/pull/381
• Add default value for types + update readme for using smoketests by @korikuzma in https://github.com/ga4gh/vrs/pull/390
• C & P error fix in CytobandInterval by @mbaudis in https://github.com/ga4gh/vrs/pull/392
• fix: get smoketests to pass by @korikuzma in https://github.com/ga4gh/vrs/pull/402
• VRS Hackathon Genotype draft by @ahwagner in https://github.com/ga4gh/vrs/pull/394
• Update validation models by @korikuzma in https://github.com/ga4gh/vrs/pull/407
• fix: models.yaml to take ordered property in account by @korikuzma in https://github.com/ga4gh/vrs/pull/409
• Add tests to check schema validation in models.yaml (#406) by @korikuzma in https://github.com/ga4gh/vrs/pull/412
• Add tests for ComposedSequenceExpression (#408) by @korikuzma in https://github.com/ga4gh/vrs/pull/413
• 1.2: Add default value for type in schemas, update smoketests readme by @korikuzma in https://github.com/ga4gh/vrs/pull/391
• Issue 404 by @ahwagner in https://github.com/ga4gh/vrs/pull/416
• relative_copy_class -> copy_assessment in CopyNumberChange example by @mbaudis in https://github.com/ga4gh/vrs/pull/419
• v1.3 release candidate by @ahwagner in https://github.com/ga4gh/vrs/pull/418

• @jsstevenson made their first contribution in https://github.com/ga4gh/vrs/pull/384
• @mbaudis made their first contribution in https://github.com/ga4gh/vrs/pull/392

Full Changelog: https://github.com/ga4gh/vrs/compare/1.2.1...1.3.0